Merge branch 'develop'

README.md

@@ -2,7 +2,7 @@
 
 # BMLSA
 
-A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm.
+A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm. May be used as a python library, or as a full command line interface.
 
 ## Features
 
@@ -13,6 +13,21 @@ A Basic multi local sequence alignment tool using the Biopython implementation o
  - Automatically align with all sequences in reference FASTA
  - All produced output is human readable!
 
+ ## Install via `pip`
+
+Just run `pip install --index-url https://git.reslate.systems/api/packages/ydeng/pypi/simple/ bmlsa` in a console that is capable of running `pip`!
+
+## CLI Demo from Git Repo
+
+Resources have been provided in this package for CI purposes, but you may use them to try out the program yourself!
+
+1. Install the program
+2. clone this repository
+3. Change into the cloned repository directory
+4. Run `bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta ./output/`
+
+The results will show up in a `output` folder (which will be generated if it doesn't exist). Use `bmlsa -h` to see what each part of the above command does!
+
 ## More Information
 
 For all live downloadable artifacts, build statuses, unit test results, and documentation, check out the continuous integration page for the [master branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/master/) ([development branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/develop/)).